Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate AZOBR_RS32405 AZOBR_RS32405 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__azobra:AZOBR_RS32405 Length = 255 Score = 191 bits (484), Expect = 2e-53 Identities = 126/267 (47%), Positives = 169/267 (63%), Gaps = 23/267 (8%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 LL+++ LT RFGGL+AV+DVS + GE+ +IGPNGAGKTTLFN ITGF P+ G +T Sbjct: 5 LLSIQGLTRRFGGLLAVSDVSATIAKGELVGLIGPNGAGKTTLFNLITGFTPPSDGTVTF 64 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS-I 129 DG++ + R P ++I+ + + RTFQN+R+F M+V +N+ V + A G S Sbjct: 65 ---DGQD-VTGRKP-WQIA-RMGMGRTFQNLRVFPNMTVFDNVSVG----AVGAFGQSPW 114 Query: 130 AGLLGLPSYTRTEREAVDLAKYW--LDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187 L+ +++R E + W L+RV L A A NL YG ++ LEIARA+ T P Sbjct: 115 RALINGGAHSRAVSE-----RSWEALERVGLTAQAGDIAANLSYGKRKYLEIARALATAP 169 Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIG--VLLIEHDMSVVMTISDHVVVLDYG 245 +L LDEPAAGLN E+ ELAD +IR H G VLL+EHDM +VM V+VL G Sbjct: 170 RLLILDEPAAGLNDTETAELAD---FIRRLHAGGVTVLLVEHDMGLVMGSCSRVIVLASG 226 Query: 246 RKISDGDPAFVKNDPAVIRAYLGEEED 272 RKI+DG P V+ DPAV+ AYLG E+D Sbjct: 227 RKIADGTPEAVQRDPAVLEAYLGVEDD 253 Lambda K H 0.319 0.137 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 210 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 294 Length of database: 255 Length adjustment: 25 Effective length of query: 269 Effective length of database: 230 Effective search space: 61870 Effective search space used: 61870 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory